"We make every effort to keep our menu prices as low as possible," In-N-Out EVP of Planning and Development Carl Van Fleet said in a statement. "Unfortunately, we have seen some pretty significant cost increases over the last year and we had to take a small price increase in order to maintain our quality standards."

Overall food prices have jumped nearly 3 percent since April, which is the highest increase in more than three years, officials said.

Other popular fast-food chains like Chipotle have also been adjusting prices.